Integrated Functional, Gene Expression and Genomic Analysis for the Identification of Cancer Targets

Abstract

The majority of new drug approvals for cancer are based on existing therapeutic targets. One approach to the identification of novel targets is to perform high-throughput RNA interference (RNAi) cellular viability screens. We describe a novel approach combining RNAi screening in multiple cell lines with gene expression and genomic profiling to identify novel cancer targets. We performed parallel RNAi screens in multiple cancer cell lines to identify genes that are essential for viability in some cell lines but not others, suggesting that these genes constitute key drivers of cellular survival in specific cancer cells. This approach was verified by the identification of PIK3CA, silencing of which was selectively lethal to the MCF7 cell line, which harbours an activating oncogenic PIK3CA mutation. We combined our functional RNAi approach with gene expression and genomic analysis, allowing the identification of several novel kinases, including WEE1, that are essential for viability only in cell lines that have an elevated level of expression of this kinase. Furthermore, we identified a subset of breast tumours that highly express WEE1 suggesting that WEE1 could be a novel therapeutic target in breast cancer. In conclusion, this strategy represents a novel and effective strategy for the identification of functionally important therapeutic targets in cancer.

Preclinical Evaluation of the WEE1 Inhibitor MK-1775 as Single-Agent Anticancer Therapy

“…However, the potential therapeutic effects of WEE1 inhibition in the absence of chemotherapies have not been widely explored. RNA interference knockdown of WEE1 is known to inhibit proliferation of cancer cell lines (13,33), and more recently, it was shown that MK-1775 alone can induce apoptosis in sarcoma cell lines treated in vitro (34). Our results similarly highlight a requirement for WEE1 activity to maintain cellular viability and genomic stability.…”

“…High expression of WEE1 was found in malignant melanoma and correlated with poor disease-free survival in this population (11). Aberrant WEE1 expression has been implicated in additional tumor types such as hepatocellular carcinoma (12), breast cancer (13), colon carcinoma (14), lung carcinoma (15), and head and neck squamous cell carcinoma (16). Advanced tumors with an increased level of genomic instability may require functional checkpoints to allow the repair of DNA perturbations that accompany genomic instability.…”

Homeobox gene IRX1 is a tumor suppressor gene in gastric carcinoma

“…Microarray analysis of experimental samples, such as gene-transfected cells, has led to identification of valuable molecular markers involved in tumor proliferation, angiogenesis, prognosis and therapeutic response (Duggan et al, 1999;Quackenbush, 2006;Perez-Diez et al, 2007;Iorns et al, 2009). Thus, we used a global cDNA microarray to identify downstream target genes of IRX1.…”

Faithful DNA Replication Requires Regulation of CDK Activity by Checkpoint Kinases

“…On the other hand, WEE1 is overexpressed in human glioblastoma and a subset of breast cancers (Iorns et al, 2009;Mir et al, 2010), and CHK1 mRNA expression was elevated in MYC-amplified neuroblastoma (Cole et al, 2010). The mechanism behind upregulation of CHK1 in MYC-amplified neuroblastoma is not known (Cole et al, 2010).…”